[gmx-users] pulling simulation

Dear Justin A. Lemkul, Thank you for answer. In US simulation the initial configurations were generated by translating ligand along the z-axis up to desired distance. Is it necessary to rotate my protein complex in correct orientation until protein exit side align with the z-axis and ligand could

Re: [gmx-users] Problem with Group and Verlet cut -off scheme

Hi, OK. A "[pairs]" interaction is a bonded interaction... so don't do that unless you need to (and probably alongside other bonded interactions involved). If you want a non-bonded interaction, you should not be specifying things in the topology. Non-bonded interactions are intrinsically spatial,

[gmx-users] problem with pull code

Dear all, >> >> I am pulling the saturated and unsaturated chains of a lipid bilayer to >> "simulate" its gel phase transition by pull code. It ends with the expected >> extended structure. >> >> But when I continue with zero pulling rate >> to maintain the extended structure for a while, the

Re: [gmx-users] Problem with Group and Verlet cut -off scheme

Hi Mark, Sorry I don't think I fully understand what you are saying. Am I correct that you are implying not to have bonded parameter for the crystal? Thank you for your suggestions and I have already done that, by that I means just using normal force field and I managed to get the crystal

Re: [gmx-users] Problem with Group and Verlet cut -off scheme

On 7/8/16 1:01 PM, Ben Tam wrote: To follow on with that I have another question, this is the error I am keep getting when I turn on pressure couple (and now too with pressure couple off) : WARNING: Listed nonbonded interaction between particles 41 and 133 at distance 4.169 which is larger

Re: [gmx-users] Problem with Group and Verlet cut -off scheme

To follow on with that I have another question, this is the error I am keep getting when I turn on pressure couple (and now too with pressure couple off) : WARNING: Listed nonbonded interaction between particles 41 and 133 at distance 4.169 which is larger than the table limit 2.000 nm. This

[gmx-users] gmx_ana_selcolletion_t definition

Hello List, I'm developing a analysis program based on tamplate.c of Gromacs 4.5.3. In order to do so, I intend to use the function gmx_ana_selcollection_evaluate() along with modification of the name field within the structure gmx_ana_selection_t inside analyze_frame function(). The

Re: [gmx-users] Problem with Group and Verlet cut -off scheme

On 7/8/16 12:05 PM, Ben Tam wrote: Dear all, My systems size is: 2.58730 2.24067 2.06100 And I am not using a pressure coupling, furthermore I did not input periodic_molecules = yes Henceforth, should I just make the system bigger? at the moment I am simulating just 574

[gmx-users] adsoption of peptide into surface

Dear Gromacs user, I want to compare the adsorption behavior of four different short peptides into a solid surface in aqueous solution to indicate which one of them has stuck stronger on the solid surface and the driving force behind the adsorption as well. The 80 ns simulations of each of them

Re: [gmx-users] adsoption of peptide into surface

On 7/8/16 12:13 PM, Alexander Alexander wrote: Dear Gromacs user, I want to compare the adsorption behavior of four different short peptides into a solid surface in aqueous solution to indicate which one of them has stuck stronger on the solid surface and the driving force behind the

Re: [gmx-users] Problem with Group and Verlet cut -off scheme

Dear all, My systems size is: 2.58730 2.24067 2.06100 And I am not using a pressure coupling, furthermore I did not input periodic_molecules = yes Henceforth, should I just make the system bigger? at the moment I am simulating just 574 molecules. Best regards, Ben

Re: [gmx-users] Problem with Group and Verlet cut -off scheme

On 7/8/16 10:54 AM, Ben Tam wrote: Hi Justin, This is what I got from the log file: Initializing Domain Decomposition on 6 ranks Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded

Re: [gmx-users] Problem with Group and Verlet cut -off scheme

Hi Justin, This is what I got from the log file: Initializing Domain Decomposition on 6 ranks Dynamic load balancing: auto Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 4.882 nm, Bond, atoms 456 457

Re: [gmx-users] Problem with Group and Verlet cut -off scheme

On 7/8/16 10:20 AM, Ben Tam wrote: Hi Mark, It shouldn't, what I am simulated is a crystal structure and my tabulated forcefield is only up to 3nm. Do you think the problem is there? To avoid the charge group, I am putting in the section of [atoms]: [ atoms ] ; nr type resnr

Re: [gmx-users] Problem with Group and Verlet cut -off scheme

Hi Mark, It shouldn't, what I am simulated is a crystal structure and my tabulated forcefield is only up to 3nm. Do you think the problem is there? To avoid the charge group, I am putting in the section of [atoms]: [ atoms ] ; nr type resnr residue atom cgnr charge mass

Re: [gmx-users] Problem with Group and Verlet cut -off scheme

Hi, Why does your topology have an interaction between atoms that are ~6 nm apart? Mark On Fri, Jul 8, 2016 at 12:37 PM Ben Tam wrote: > Hi Mark, > > > Thank you for your reply and your suggestion. Now I get it working, I have > another problem. This error pops up when

[gmx-users] lipid pulling

Dear all, It is just I forgot to delete the pull-coord-init part. But after I delete the followinf lines, === >> pull-coord1-init= 1.0 >> pull-coord2-init= 1.0 >> pull-coord3-init= 1.0 >> pull-coord4-init= 1.0

Re: [gmx-users] gmx_saxs sampling frequency

Yu, Thanks for the idea. I see that gmx_sans allows for an optional data file input "nsfactor.dat" but am unsure what that does. Could you provide some details into what exactly goes into the "nsfactor.dat" file and what the output would be? Thanks for your help. Regards, Evan L. On Jul 8, 2016

Re: [gmx-users] Residue Numbers

On 7/7/16 11:37 AM, Amali Guruge wrote: Dear All, I used g_mmpbsa for free energy calculations. I competed contribution of residues to the binding energy using python script. Original residue number is available in final_contrib_energy.dat file. But we use energyMapIn.dat file for the graph

Re: [gmx-users] new residue went into crash during energy minimization

On 7/7/16 10:08 PM, Wang Tao wrote: Hello,everyone! I am using charmm27 in gromacs for simulation of a double strand DNA , of which a residue is modified by a group.The forcefield parameters for the new residue is generated with swissparam. After conducting energy minimization , i checked

Re: [gmx-users] Hbond occupancy

On 7/8/16 9:01 AM, Amali Guruge wrote: Thank you very much Eric for the answer. Could you please give information regarding to the command use in this calculation? Thank you. You can't get, e.g. % occupancy directly but the gmx hbond output (-hbn -hbm) can be post-processed with a simple

Re: [gmx-users] Hbond occupancy

Thank you very much Eric for the answer. Could you please give information regarding to the command use in this calculation? Thank you. On Fri, Jul 8, 2016 at 5:31 PM, Erik Marklund wrote: > gmx hbond > > > On 8 Jul 2016, at 12:24, Amali Guruge

[gmx-users] Selection of cylindrical shape

Dear gromacs user, I am working with Protein water binary system.During simulation my Protein formed a cylindrical shape surrounded by water molecule and some water molecule got stuck within the cylindrical Protein. So,I need to visualize and analyse the cylindrical shaped protein and water

Re: [gmx-users] Multi GPU Workstation with 4 Way SLI

Hi, have a look at https://www.mpibpc.mpg.de/15070156/Kutzner_2015_JCC.pdf which should answer your questions! Best, Carsten > On 08 Jul 2016, at 12:11, Nikhil Maroli wrote: > > Dear all, > > > > We have a budget of $12,000. for GPU Workstation. We will be running

Re: [gmx-users] Hbond occupancy

gmx hbond > On 8 Jul 2016, at 12:24, Amali Guruge wrote: > > Dear All, > > Can anyone know how to calculate H bond occupancy with Gromacs? > > Thank you > -- > Gromacs Users mailing list > > * Please search the archive at >

Re: [gmx-users] gmx_saxs sampling frequency

Hi Evan, I had the same issue, and could not solve the problem as I did not go into the source code. What I did at that time is to use "gmx sans" with modified nsfactor.dat where I put atomic number instead of scattering length, though I don't know how appropriate that approach is.. Yu

Re: [gmx-users] Problem with Group and Verlet cut -off scheme

Hi Mark, Thank you for your reply and your suggestion. Now I get it working, I have another problem. This error pops up when I do: gmx mdrun -table table6-12.xvg -tablep table_Mg_O4.xvg This is the error I am getting. I am trying to understand it, but I don't understand how to solve it:

[gmx-users] eneconv and timestamps

Hi, I don't understand the behaviour of eneconv(_d) in Gromacs 4.6.7 I have a long trajectory saved every .5ps in single precision and want to save it every ps. Unfortunately, there is no -skip option. So, I figured with your help some time ago to first save the edr file in double precision using

[gmx-users] Hbond occupancy

Dear All, Can anyone know how to calculate H bond occupancy with Gromacs? Thank you -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For

[gmx-users] Multi GPU Workstation with 4 Way SLI

Dear all, We have a budget of $12,000. for GPU Workstation. We will be running Gromacs for MD especially in Membrane protein system.Kindly give the suggestions for the below 1. Provide me the suggestion for the below configuration / There will be any load imbalance with processor and GPU

Re: [gmx-users] Position restraints for water during EM

Hi Gregory, There is no default position restraint during EM. Of course, one wouldn't expect them to move much and one would expect the local energy minimum to be rather close to the initial position, if you used an equilibrated water box to set up the system. Cheers, Tsjerk On Jul 8, 2016

[gmx-users] Position restraints for water during EM

Hello all: I would like to know where it is specified that waters are position-restrained during energy minimization. I can see that there is a #ifdef block for restraining the water, but I don't know where it is actually called. The .mdp files I use for EM (which I adapted from tutorials)